Quote alignment parameters during align subcommand. This should addre…

…ss issue #52.
EichlerLab · Dec 2, 2016 · 66086c1 · 66086c1
1 parent 8090723
commit 66086c1
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/bin/smrtsv.py b/bin/smrtsv.py
@@ -152,7 +152,7 @@ def align(args):
         "batches=%s" % args.batches,
         "threads=%s" % args.threads,
         "tmp_dir=%s" % args.tmpdir,
-        "alignment_parameters=%s" % args.alignment_parameters
+        "alignment_parameters=\"%s\"" % args.alignment_parameters
     )
 
 def detect(args):